Question: How to perform FPKM on raw reads in R
gravatar for manish20072013
3.7 years ago by
manish2007201310 wrote:

How I perform fpkm on a file containing the raw reads of two samples and each sample have three replicates? I want to do the analysis in R.

sequencing rna-seq fpkm R • 6.6k views
ADD COMMENTlink modified 23 months ago by Ahmed Alhendi50 • written 3.7 years ago by manish2007201310
gravatar for Istvan Albert
3.7 years ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

See the blog post "What the FPKM" by Harold Pimentel that also provides R code:

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Istvan Albert ♦♦ 86k
gravatar for Ahmed Alhendi
23 months ago by
University of Southampton, UK
Ahmed Alhendi50 wrote:

Try countToFPKM package. This package provides an easy to use function to convert the read count matrix into FPKM values normalised by library size and feature effective length. It also provides the user with a reliable function to generate FPKM heatmap plot of the highly variable features in RNA-Seq dataset.; following the equation:

enter image description here.

The fpkm() function requires three inputs to return FPKM as numeric matrix normalized by library size and feature length:

  • counts A numeric matrix of raw feature counts.
  • featureLength A numeric vector with feature lengths that can be obtained using biomaRt.
  • meanFragmentLength A numeric vector with mean fragment lengths, which can be calculate with
    Picard using CollectInsertSizeMetrics.

Also see

ADD COMMENTlink written 23 months ago by Ahmed Alhendi50

Could the countToFPKM package work for single end RNA seq data too? Thanks.

ADD REPLYlink written 11 days ago by salehm0
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